Nemo  2.3.46
individual.h
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1 
30 #ifndef INDIVIDUAL_H
31 #define INDIVIDUAL_H
32 #include <map>
33 #include <deque>
34 #include <limits>
35 #include "types.h"
36 #include "ttrait.h"
37 #include "ttrait_with_map.h"
38 #include "binarystoragebuffer.h"
39 
49 class Individual {
50 private:
52  unsigned long _id;
54  unsigned short _age;
58  unsigned long _motherID, _fatherID;
62  unsigned short _home;
70  unsigned char _pedigreeClass;
72  double _fecundity;
74  unsigned short _matings[5];
76  unsigned short _realizedFecundity[5];
78  unsigned int _trait_nb;
79 
80 public:
81 
83  static unsigned long currentID;
84 
85  typedef int IDX;
86 
88  std::deque<TTrait*> Traits;
89 
90  Individual ();
95  Individual* init ();
100  void reset ();
101 
104  void setID (unsigned long value) {_id = value;}
105  void setAge (unsigned short value) {_age = value;}
106  void Aging () {_age++;}
107  void setFatherID (unsigned long value) {_fatherID = value;}
108  void setMotherID (unsigned long value) {_motherID = value;}
109  void setFather (Individual* f) {_father = f;}
110  void setMother (Individual* m) {_mother = m;}
111  void setHome (unsigned short value) {_home = value;}
112  void setSex (sex_t sex) {_sex = sex;}
113  void setCurrentID (unsigned long value) {currentID = value;}
114  void setIsSelfed (bool s) {_pedigreeClass = (s ? 4 : 0);}
115  void setPedigreeClass (Individual* mother, Individual* father) {_pedigreeClass = getPedigreeClass(mother,father);}
116  void setPedigreeClass (unsigned char ped) {_pedigreeClass = ped;}
117 
119 
122  unsigned long getID () {return _id;}
123  unsigned short getAge () {return _age;}
124  unsigned long getFatherID () {return _fatherID;}
125  unsigned long getMotherID () {return _motherID;}
128  unsigned short getHome () {return _home;}
129  sex_t getSex () {return _sex;}
130  bool isFemale () {return (_sex == FEM);}
131  bool getIsSelfed () {return (_pedigreeClass == 4);}
132  unsigned long getcurrentID () {return currentID;}
133  double getFecundity () {return _fecundity;}
142  unsigned short getMatings (unsigned int cat)
143  {
144  return _matings[cat];
145  }
147  unsigned short getLocalMatings ( )
148  {
149  return _matings[1]+_matings[2]+_matings[3]+_matings[4];
150  }
152  unsigned int getTotMatings ( )
153  {
154  return _matings[0] + getLocalMatings();
155  }
164  unsigned short getRealizedFecundity (unsigned int cat)
165  {
166  return _realizedFecundity[cat];
167  }
168 
171  {
172  return _realizedFecundity[1]+_realizedFecundity[2]+_realizedFecundity[3]+_realizedFecundity[4];
173  }
174 
176  unsigned int getTotRealizedFecundity( ) {return _realizedFecundity[0] + getLocalRealizedFecundity( );}
177 
179  unsigned int getPedigreeClass ( )
180  {
181  return _pedigreeClass;
182  }
193  unsigned int getPedigreeClass (Individual* mother, Individual* father);
195 
198  void store_data ( BinaryStorageBuffer* saver );
199 
200  void retrieve_data ( BinaryStorageBuffer* reader );
202 
205 
207  double setFecundity (double value) {_fecundity = value; return value;}
208 
210  void reset_counters ( )
211  {
212  for(unsigned int i = 0; i < 5; i++) {
213  _matings[i] = 0; _realizedFecundity[i] = 0;
214  } }
215 
219  void addMating (unsigned int category)
220  { _matings[category]++; }
221 
225  void DidHaveABaby (unsigned int category)
226  { _matings[category]++; _realizedFecundity[category]++; }
227 
230  {
231  unsigned short mate = getLocalMatings();
232  return (mate != 0 ? (double) getLocalRealizedFecundity()/mate : 0.0);
233  }
238  {
239  return (_matings[0] != 0 ? (double) _realizedFecundity[0]/_matings[0] : 0.0);
240  }
242 
245 
247  unsigned int getTraitNumber() { return _trait_nb;}
248 
251  std::deque<TTrait *>& getTraits() {return Traits;}
252 
256  void* setTrait (IDX T, void* value)
257  { return getTrait(T)->set_trait(value); }
258 
261  void setTraitValue (IDX T)
262  { getTrait(T)->set_value(); }
263 
265  void setTraitValue ()
266  { for(unsigned int i = 0; i < _trait_nb; i++) Traits[i]->set_value(); }
267 
271  void* getTraitValue (IDX T)
272  { return getTrait(T)->getValue(); }
273 
277  TTrait* getTrait (IDX T)
278  { if( T == -1 || !(T < (int)_trait_nb) )
279  fatal("Individual::Trying to access a trait not present in the traits table (at %i, size %i)\n",T,_trait_nb);
280  return Traits[T];
281  }
282 
288  void addTrait (TTrait* theTrait, IDX pos)
289  { if((int)_trait_nb != pos)
290  fatal("Individual::adding a trait to the wrong position (at %i, size %i)!\n",pos,_trait_nb);
291  Traits.push_back(theTrait); _trait_nb++;
292  }
293 
296  void removeTrait (IDX T)
297  { delete Traits[T]; Traits.erase(Traits.begin() + T); _trait_nb--;}
298 
300  void clearTraits ( )
301  { if(_trait_nb != 0) {for(unsigned int i = 0; i < Traits.size(); ++i) delete Traits[i];
302  Traits.clear(); _trait_nb = 0;}
303  }
304 
309  void inheritTrait (IDX T, Individual* mother, Individual* father)
310  {
311  recombine(_id);
312  getTrait(T)->inherit(mother->getTrait(T), father->getTrait(T));
313  }
314 
317  void mutateTrait (IDX T)
318  { getTrait(T)->mutate(); }
319 
325  void createTrait (IDX i, Individual* mother, Individual* father)
326  { if(!(mother && father))
327  fatal("Individual::create::received null pointer!!!\n");
328  TTrait* T = Traits[i];
329  recombine(_id);
330  T->inherit(mother->getTrait(i),father->getTrait(i));
331  T->mutate();
332  T->set_value();
333  }
334 
339  Individual* createTrait (IDX i, bool do_inherit, bool do_mutate)
340  {
341  if(do_inherit) inheritTrait(i, _mother, _father);
342  if(do_mutate) mutateTrait(i);
343  setTraitValue(i);
344  return this;
345  }
346 
349  {
350  for(unsigned int i = 0; i < _trait_nb; i++) {
351  Traits[i]->init_sequence();
352  Traits[i]->set_value();
353  }
354  //we have to set the parents ids otherwise the first offspring generation will be made of full sibs only.
355  static unsigned long ID = std::numeric_limits< unsigned long >::max();
356  _motherID = ID--;
357  _fatherID = ID--;
358  return this;
359  }
360 
363  {
364  inherit(_mother, _father);
365  mutate();
366  setTraitValue();
367  return this;
368  }
372  Individual* create (bool do_inherit, bool do_mutate)
373  {
374  if(do_inherit) inherit(_mother, _father);
375  if(do_mutate) mutate();
376  setTraitValue();
377  return this;
378  }
379 
384  {
385  if(!(mother && father))
386  fatal("Individual::create::received null parents pointer!!!\n");
387  TTrait *TT;
388  recombine(_id);
389  for(unsigned int i = 0; i < _trait_nb; i++) {
390  TT = Traits[i];
391  TT->inherit(mother->getTrait(i), father->getTrait(i));
392  TT->mutate();
393  TT->set_value();
394  }
395  return this;
396  }
397 
401  void inherit (Individual* mother, Individual* father)
402  {
403  recombine(_id);
404  for(unsigned int i = 0; i < _trait_nb; i++)
405  Traits[i]->inherit(mother->getTrait(i), father->getTrait(i));
406  }
407 
409  void mutate ()
410  { for(unsigned int i = 0; i < _trait_nb; i++) Traits[i]->mutate(); }
411 
412  void recombine (unsigned long ID)
415 
417  void show_up();
418 
420  Individual* clone ();
421 
424 
425  Individual& operator=(const Individual& i);
427  bool operator==(const Individual& i);
428  bool operator!=(const Individual& i);
430 };
431 
432 #endif //INDIVIDUAL_H
433 
void setIsSelfed(bool s)
Definition: individual.h:114
virtual void inherit(TTrait *mother, TTrait *father)=0
Inheritance procedure, creates a new trait from mother's and father's traits.
virtual void * set_trait(void *value)=0
Called to set the phenotypic to a particular value or to give context-dependant value(s) to the trait...
std::deque< TTrait * > & getTraits()
Accessot to the traits table itself.
Definition: individual.h:251
void * getTraitValue(IDX T)
Accessor to the value (phenotype) of a particular trait.
Definition: individual.h:271
unsigned short _home
Natal Patch tag.
Definition: individual.h:62
unsigned int getTotRealizedFecundity()
Gives the total number of surviving offspring for all categories of mating.
Definition: individual.h:176
void inheritTrait(IDX T, Individual *mother, Individual *father)
Calls the inheritance procedure of a particular trait.
Definition: individual.h:309
void store_data(BinaryStorageBuffer *saver)
Definition: individual.cc:102
void show_up()
Write some info to stdout.
Definition: individual.cc:132
unsigned long _motherID
Parents ID tags.
Definition: individual.h:58
unsigned int getTotMatings()
Gives the total number of matings of an individual.
Definition: individual.h:152
unsigned long getID()
Definition: individual.h:122
void setFather(Individual *f)
Definition: individual.h:109
Individual()
Definition: individual.cc:41
virtual void mutate()=0
Mutation procedure, perform mutations on the genes sequence.
unsigned short _age
Age.
Definition: individual.h:54
unsigned short getRealizedFecundity(unsigned int cat)
Gives the number of surviving offspring for a given pedigree class of mating.
Definition: individual.h:164
unsigned short getLocalMatings()
Gives the number of times an individual mated with an individual from the same patch.
Definition: individual.h:147
unsigned long _id
ID tag, unique for one simulation.
Definition: individual.h:52
void setFatherID(unsigned long value)
Definition: individual.h:107
TTrait * getTrait(IDX T)
Trait accessor.
Definition: individual.h:277
void * setTrait(IDX T, void *value)
Sets the phenotype/value of a trait to a particular value.
Definition: individual.h:256
Individual * getFather()
Definition: individual.h:126
unsigned int _trait_nb
Number of traits in the table.
Definition: individual.h:78
unsigned long getMotherID()
Definition: individual.h:125
void setMotherID(unsigned long value)
Definition: individual.h:108
Individual * getMother()
Definition: individual.h:127
unsigned int getLocalRealizedFecundity()
Gives the total number of surviving offspring when mating occures with mates of the same patch...
Definition: individual.h:170
void setPedigreeClass(Individual *mother, Individual *father)
Definition: individual.h:115
Interface for all trait types, declares all basic trait operations.
Definition: ttrait.h:46
void reset()
Resets parameters and traits values.
Definition: individual.cc:79
void fatal(const char *str,...)
Definition: output.cc:90
void setID(unsigned long value)
Definition: individual.h:104
Individual * _father
Definition: individual.h:60
Individual * create_first_gen()
Creates an individual's genotypes and phenotypes for first generation.
Definition: individual.h:348
unsigned short _matings[5]
Mating counter.
Definition: individual.h:74
unsigned long getFatherID()
Definition: individual.h:124
unsigned int getTraitNumber()
Accessor to the size of the traits table.
Definition: individual.h:247
Individual * create(Individual *mother, Individual *father)
Creates an individual, inherit, mutate and set all its trait's values.
Definition: individual.h:383
void setMother(Individual *m)
Definition: individual.h:110
void clearTraits()
Clears the traits container.
Definition: individual.h:300
void createTrait(IDX i, Individual *mother, Individual *father)
Sets a particular trait's genotype and phenotype values from the two parents.
Definition: individual.h:325
unsigned long getcurrentID()
Definition: individual.h:132
double _fecundity
Assigned fecundity.
Definition: individual.h:72
void DidHaveABaby(unsigned int category)
Increments the mating and realized fecundity counters according to the pedigree class of the offsprin...
Definition: individual.h:225
unsigned short getAge()
Definition: individual.h:123
void recombine(unsigned long ID)
Definition: individual.h:412
Individual * create()
Creates an individual's genotypes and phenotypes with recombination and mutations.
Definition: individual.h:362
Individual & operator=(const Individual &i)
Assignment, make a deep copy of the parameter values and traits.
Definition: individual.cc:161
void Aging()
Definition: individual.h:106
static void recombine(unsigned long indID)
Definition: ttrait_with_map.cc:485
unsigned short _realizedFecundity[5]
Number of surviving offspring from the different mating categories (see matings). ...
Definition: individual.h:76
sex_t
Sex types, males are always 0 and females 1!!
Definition: types.h:36
Individual * createTrait(IDX i, bool do_inherit, bool do_mutate)
Creates an individual's genotypes and phenotypes with optional recombination or mutations on one trai...
Definition: individual.h:339
double setFecundity(double value)
Sets the fecundity to the value given and returns it.
Definition: individual.h:207
A class to store any kind of data in a char buffer before unloading it in a binary data file...
Definition: binarystoragebuffer.h:40
virtual void * getValue() const =0
Genotype to phenotype mapper.
unsigned int getPedigreeClass()
Returns the pedigree class of the individual, as set during offspring creation.
Definition: individual.h:179
bool getIsSelfed()
Definition: individual.h:131
Individual * create(bool do_inherit, bool do_mutate)
Creates an individual's genotypes and phenotypes with optional recombination or mutations.
Definition: individual.h:372
void reset_counters()
Resets the mating and fecundity counters.
Definition: individual.h:210
virtual void set_value()=0
Tells the trait to set its phenotype from genotype, should be used instead of getValue().
static unsigned long currentID
The ID counter, reset at the beginning of each simulation.
Definition: individual.h:83
sex_t _sex
Sex tag.
Definition: individual.h:56
void setSex(sex_t sex)
Definition: individual.h:112
unsigned short getHome()
Definition: individual.h:128
bool operator==(const Individual &i)
Only checks for traits equivalence.
Definition: individual.cc:195
double getFecWithHomePatchMate()
Returns the proportion of succesfull local matings (i.e.
Definition: individual.h:229
Individual * _mother
Parents pointers.
Definition: individual.h:60
void removeTrait(IDX T)
Removes a trait from the table.
Definition: individual.h:296
void setTraitValue()
Calls the value setting procedure of all traits present in an individual.
Definition: individual.h:265
double getFecundity()
Definition: individual.h:133
void mutateTrait(IDX T)
Calls the mutation procedure of a particular trait.
Definition: individual.h:317
bool isFemale()
Definition: individual.h:130
void inherit(Individual *mother, Individual *father)
Calls the inheritance procedure of all the traits present in the individual.
Definition: individual.h:401
void retrieve_data(BinaryStorageBuffer *reader)
Definition: individual.cc:117
void setHome(unsigned short value)
Definition: individual.h:111
void setTraitValue(IDX T)
Calls the value setting procedure of a particular trait.
Definition: individual.h:261
void setAge(unsigned short value)
Definition: individual.h:105
void setPedigreeClass(unsigned char ped)
Definition: individual.h:116
int IDX
Definition: individual.h:85
unsigned long _fatherID
Definition: individual.h:58
Individual * init()
Inits parameters and traits.
Definition: individual.cc:53
sex_t getSex()
Definition: individual.h:129
void mutate()
Calls the mutation procedure of all the traits present in the individual.
Definition: individual.h:409
void addTrait(TTrait *theTrait, IDX pos)
Adds a trait to the table.
Definition: individual.h:288
unsigned short getMatings(unsigned int cat)
Gives the number of matings that individual had with mates from a given pedigree class.
Definition: individual.h:142
This class contains traits along with other individual information (sex, pedigree, etc. ).
Definition: individual.h:49
Definition: types.h:37
~Individual()
Definition: individual.h:91
unsigned char _pedigreeClass
Pedigree class of the individual.
Definition: individual.h:70
void setCurrentID(unsigned long value)
Definition: individual.h:113
std::deque< TTrait * > Traits
The traits table.
Definition: individual.h:88
bool operator!=(const Individual &i)
Definition: individual.cc:210
void addMating(unsigned int category)
Increments the mating counter according to the pedigree class of the offspring.
Definition: individual.h:219
double getFecWithOtherPatchMate()
Returns the proportion of successfull remote matings.
Definition: individual.h:237
Individual * clone()
Cloning procedure, clones all the traits present in the individual.
Definition: individual.cc:149

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